Module: ncbi.datasets.openapi.api.taxonomy_api

NCBI Datasets API

Module: ncbi.datasets.openapi.api.taxonomy_api

NCBI Datasets API

### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets API is still in alpha, and we’re updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated bag](https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/datasets/docs/rehydrate/), and retrieve the individual data files at a later time. # noqa: E501

The version of the OpenAPI document: v1 Generated by: https://openapi-generator.tech

class ncbi.datasets.openapi.api.taxonomy_api.TaxonomyApi(api_client=None)

Bases: object

NOTE: This class is auto generated by OpenAPI Generator Ref: https://openapi-generator.tech

Do not edit the class manually.

tax_name_query(taxon_query, **kwargs)

Get a list of taxonomy names and IDs given a partial taxonomic name # noqa: E501

This endpoint retrieves a list of taxonomy names and IDs given a partial taxonomic name of any rank. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.tax_name_query(taxon_query, async_req=True)
>>> result = thread.get()
Parameters

taxon_query (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

Keyword Arguments
  • tax_rank_filter (V1OrganismQueryRequestTaxRankFilter) – Set the scope of searched tax ranks. [optional]

  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

  • _preload_content (bool) – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout (int/float/tuple) – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

V1SciNameAndIds

If the method is called asynchronously, returns the request thread.

taxonomy_filtered_subtree(taxons, **kwargs)

Use taxonomic identifiers to get a filtered taxonomic subtree # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_filtered_subtree(taxons, async_req=True)
>>> result = thread.get()
Parameters

taxons ([str]) –

Keyword Arguments
  • specified_limit (bool) – Limit to specified species. [optional]

  • rank_limits ([V1OrganismRankType]) – Limit to the provided ranks. If empty, accept any rank.. [optional]

  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

  • _preload_content (bool) – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout (int/float/tuple) – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

V1TaxonomyFilteredSubtreeResponse

If the method is called asynchronously, returns the request thread.

taxonomy_filtered_subtree_post(v1_taxonomy_filtered_subtree_request, **kwargs)

Use taxonomic identifiers to get a filtered taxonomic subtree by post # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_filtered_subtree_post(v1_taxonomy_filtered_subtree_request, async_req=True)
>>> result = thread.get()
Parameters

v1_taxonomy_filtered_subtree_request (V1TaxonomyFilteredSubtreeRequest) –

Keyword Arguments
  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

  • _preload_content (bool) – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout (int/float/tuple) – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

V1TaxonomyFilteredSubtreeResponse

If the method is called asynchronously, returns the request thread.

taxonomy_metadata(taxons, **kwargs)

Use taxonomic identifiers to get taxonomic metadata # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_metadata(taxons, async_req=True)
>>> result = thread.get()
Parameters

taxons ([str]) –

Keyword Arguments
  • returned_content (V1TaxonomyMetadataRequestContentType) – Return either tax-ids alone, or entire taxononmy-metadata records. [optional]

  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

  • _preload_content (bool) – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout (int/float/tuple) – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

V1TaxonomyMetadataResponse

If the method is called asynchronously, returns the request thread.

taxonomy_metadata_post(v1_taxonomy_metadata_request, **kwargs)

Use taxonomic identifiers to get taxonomic metadata by post # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_metadata_post(v1_taxonomy_metadata_request, async_req=True)
>>> result = thread.get()
Parameters

v1_taxonomy_metadata_request (V1TaxonomyMetadataRequest) –

Keyword Arguments
  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

  • _preload_content (bool) – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout (int/float/tuple) – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

V1TaxonomyMetadataResponse

If the method is called asynchronously, returns the request thread.

Generated October 22, 2021